04-DE.Rmd

# Differential expression, FDR, GO, and GSEA {#de}

**DESeq2** is a popular and accurate computational algorithm to detect differential gene expression from RNA-seq data. It includes many elegant quantitative considerations, such as:  

- Normalize the gene read counts by library size and composition  
- Model gene read counts with negative binomial distribution  
- Use hierarchical modeling to stabilize the gene variance  
- Use Benjamini-Hochberg to calculate control for false discovery rate of calling differentially expressed genes  
- Filter lowly expressed genes to reduce the number of hypotheses to be tested  

## DESeq2 library normalization

<iframe width="560" height="315" src="https://www.youtube.com/embed/UFB993xufUU?start=14" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## DESeq2 variance stabilization

<iframe width="560" height="315" src="https://www.youtube.com/embed/CYHTR1IxwBc" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## Multiple hypotheses testing and False Discovery Rate

<iframe width="560" height="315" src="https://www.youtube.com/embed/wtU_8UQVZM8" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## DESeq2 gene filtering

<iframe width="560" height="315" src="https://www.youtube.com/embed/Gi0JdrxRq5s?start=19" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## Gene Ontology (GO analysis)

<iframe width="560" height="315" src="https://www.youtube.com/embed/Q5X934l9vY8" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## Gene Set Enrichent Analysis (GSEA)

<iframe width="560" height="315" src="https://www.youtube.com/embed/dZja6aeTxpc" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

## DESeq2 tutorial

<iframe width="560" height="315" src="https://www.youtube.com/embed/EJ0MQf7_O4U" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>